Posted by Genetics, on 11 January 2021
The International C. elegans Conference takes place every two years and features cutting-edge research in a diverse array of topics, including physiology, neurobiology, development, evolution, behavior, aging, ecology, gene regulation, genomics, and more. For 2021, #Worm21 has been reimagined for a virtual platform and will focus on early career researchers at every stage.
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Posted by the Node, on 11 January 2021
We’re happy to confirm the next webinar in our Development presents… series will be chaired by our Editor Swathi Arur (The University of Texas MD Anderson Cancer Center), who has brought together talks that span her interests in C. elegans development, the germline and cell signalling.
Brandon Scott Carpenter (from David Katz’s lab at Emory University School of Medicine)
‘C. elegans establishes germline versus soma by balancing inherited histone methylation’
Hayao Ohno (from Zhirong Bao’s lab at the Sloan Kettering Institute)
‘Small RNAs couple embryonic developmental programs to gut microbes’
Swann Floc’hlay (formerly in Denis Thieffry’s lab at IBENs)
‘Deciphering and modelling the TGF-beta signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo’
The webinar will be held in Remo, our browser-based conferencing platform – after the talks you’ll have the chance to meet the speakers and other participants at virtual conference tables. If you can’t make it on the day, talks will be available to watch for a couple of weeks after the event (look out for details on the Node).
Feel free to share this poster with your colleagues:
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Posted by the Node, on 11 January 2021
Various organisations and looser assemblies of locked down researchers have begun to put together online seminar and talk series, many of which are open to anyone (usually with registration), and many of which also have previous talks recorded.
Here’s a list of what we’ve found recently, developmental biology and adjacent – please let us know if we missed anything so we can keep it up to date. For upcoming virtual developmental biology conferences/symposia, see our Events calendar page.
First up from us is Development presents…, the webinar series hosted each month by a different Development Editor which will be a platform for early career researchers to share their work. As well as the talks, you also have the chance to meet the speakers and other participants at interactive video tables – giving the developmental biology community the chance to network virtually.
The next webinar will be Wednesday 13 January, 16.00 GMT, hosted by Swathi Arur and featuring talks from Brandon Scott Carpenter, Hayao Ohno and Swann Floc’hlay.
SDB monthly postdoc seminar series.
Next talk: February 12, Melissa LaBonty & Adam Isabella
Morphogenesis Seminar Series, University of Cambridge
Next talk: January 18, Anna Erzberger
Optical Biology 2021 Seminar Series
Next talk: January 27, Pavel Tomancak
New PIs In Cell-Dev-Biol forum
Next talk: January 15th, Felicity Davis. Check out the poster above for full 2021 list – all the way to December!
February 1 13:30 – 18:30(JST/KST), 12:30 – 17:30(CST)
Teaching Dev Bio Forum
With Michael Barresi – next session is January 28 – email mbarresi@smith.edu to gain access.
MiR@W Day: Modelling and measuring the landscapes of early embryonic development
January 25 – The workshop will run from 14:00 until 18:15
Neural Crest Research Colloquia
Next talk: January 19, Marcos Simoes-Costa
Weinstein Cardiovascular Development & Regeneration
Next talk tbc
Zebrafish Disease Models Society Virtual Seminars
Next talk: January 12, Xiao Zhao, Rosa Uribe and Olov Andersson
January 19
Vertebrate Gastrulation Zoom Talks
Next talk: January 14, Ray Keller & Karen Kasza
Next talk: January 12, Stephan Beck.
Plantae Presents – A New Global Plant Science Talk Series
Next talk: January 20 – Short talks on specialised metabolites.
Now accepting applications for Feb-April
GARNet-Presents Plant Science Webinar
Next talk: January 12, Sarah Blackford
Flatworm Fridays – a trainee-centered virtual series focused on flatworms and related critters
Next talk: February 26
Spiraliabase Virtual Lab Meetings
Next meeting: 11 February, SEM and TEM imaging.
Next talks: January 20, Chiara Sinigaglia & Dylan Faltine-Gonzales
Next talk: January 13, Maggie Chasse & Fred Winston
2020 BSCB GenSoc UK Cilia Network e-Symposium
Next talk: January 12, Muneyoshi Ichikawa, Sónia Gomes Pereira, Monica Veneres, Alexandre Dumoulin, Thao Phan, Philippe Bastin
World Wide Neuro – Neuroscience seminars online
Next devbio talk: January 11, Ryusuke Niwa
Neuro Zoom: lively neuroscience research talks every week
Next talk: Janurary 11: Kaiwen He & Juan Song
BPPB (Biological Physics/Physical Biology) Seminars
Next talk: January 15, Robijn Bruinsma
Next talk: January 12, Craig Morrell
International Zebrafish Society Webinars
Next talk: January 14, Evolutionary Studies:
Just Under the Surface: Leveraging Zebrafish to Understand the Interplay Between Evolution and Development
Next talks: January 19, Xili Lui.
Cell Migration Virtual Seminars
Next talk: January 11, Helen Blau
Next talk: January 13, Helene Bouvrais & Arne Gennerich
Aging Science Talks: Science for the Community
Next talk: January 20, How aging and disease drive stem cell dysfunction
MicroSeminar- Free Web-based Microbiology Seminar Series
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Posted by Katherine Brown, on 6 January 2021
Closing Date: 15 March 2021
We currently have an opening for a Reviews Editor as a maternity cover position on Development. As this is a temporary position, we are specifically looking for candidates with editorial experience.
Core responsibilities of the position include:
For further details and instructions on how to apply, please see the full job advert here. If you are interested in applying, but would like further information or have any questions, please feel free to drop me an email.
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Posted by the Node, on 6 January 2021
Welcome to our monthly trawl for developmental biology (and related) preprints.
The preprints this month are hosted on bioRxiv and arXiv – use these links to get to the section you want.
| Stem cells, regeneration & disease modelling
Vangl2 regulates the dynamics of Wnt cytonemes in vertebrates
Lucy Brunt, Gediminas Greicius, Benjamin D Evans, David M Virshup, Kyle CA Wedgwood, Steffen Scholpp
Sox2 levels configure the WNT response of epiblast progenitors responsible for vertebrate body formation
Robert Blassberg, Harshil Patel, Thomas Watson, Mina Gouti, Vicki Metzis, M Joaquina Delás, James Briscoe
Wnt/beta-catenin signalling is dispensable for adult neural stem cell homeostasis and activation
Sophie H. L. Austin, Lachlan Harris, Oana Paun, Piero Rigo, François Guillemot, Noelia Urbán
Knockout of myoc reveals the role of myocilin in zebrafish sex determination associated with Wnt signalling downregulation
Raquel Atienzar-Aroca, José-Daniel Aroca-Aguilar, Susana Alexandre-Moreno, Jesús-José Ferre-Fernández, Juan-Manuel Bonet-Fernández, María-José Cabañero-Varela, Julio Escribano
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SOX7 deficiency causes ventricular septal defects through its effects on endocardial-to-mesenchymal transition and the expression of Wnt4 and Bmp2
Andrés Hernández-García, Sangbae Kim, Yumei Li, Bum Jun Kim, Hitisha P. Zaveri, Valerie K. Jordan, M. Cecilia Ljungberg, Rui Chen, Rainer B. Lanz, Daryl A. Scott
Proteomic analysis identifies the E3 ubiquitin ligase Pdzrn3 as a regulatory target of Wnt5a-Ror signaling
Sara E. Konopelski Snavely, Michael W. Susman, Ryan C. Kunz, Jia Tan, Srisathya Srinivasan, Michael D. Cohen, Kyoko Okada, Helen Lamb, Shannon S. Choi, Edith P. Karuna, Michael K. Scales, Steven P. Gygi, Michael E. Greenberg, Hsin-Yi Henry Ho
Genomic analyses reveal FoxG as an upstream regulator of wnt1 required for posterior identity specification in planarians
E. Pascual-Carreras, M. Marín-Barba, S. Castillo-Lara, P. Coronel-Córdoba, M.S. Magri, G.N. Wheeler, J.F. Abril, J.L. Gomez-Skarmeta, E. Saló, T. Adell
Extracellular spreading of Wingless is required for Drosophila oogenesis
Xiaoxi Wang, Kimberly S. LaFever, Indrayani Waghmare, Andrea Page-McCaw
Canonical Wnt signaling exerts bidirectional control on choroid plexus epithelial development
Arpan Parichha, Varun Suresh, Mallika Chatterjee, Aditya Kshirsagar, Lihi Ben-Reuven, Tsviya Olender, M. Mark Taketo, Velena Radosevic, Mihaela Bobic-Rasonja, Sara Trnski, Nataša Jovanov Milošević, Orly Reiner, Shubha Tole
The Wnt effector TCF7l2 promotes oligodendroglial differentiation by repressing autocrine BMP4-mediated signaling
Sheng Zhang, Yan Wang, Xiaoqing Zhu, Lanying Song, Xinhua Zhan, Edric Ma, Jennifer McDonough, Hui Fu, Franca Cambi, Judith Grinspan, Fuzheng Guo
Notch signaling is a critical initiator of roof plate formation as revealed by the use of RNA profiling of the dorsal neural tube
Shai Ofek, Sophie Wiszniak, Sarah Kagan, Markus Tondl, Quenten Schwarz, Chaya Kalcheim
Ubiquitin-protein ligase Ubr5 cooperates with Hedgehog signalling to promote skeletal tissue homeostasis
David Mellis, Katherine A Staines, Silvia Peluso, Ioanna Ch. Georgiou, Natalie Dora, Malgorzata Kubiak, Michela Grillo, Colin Farquharson, Elaine Kinsella, Anna Thornburn, Stuart H Ralston, Donald M Salter, Natalia A Riobo-Del Galdo, Robert E Hill, Mark Ditzel
Non-cell autonomous inhibition of the Shh pathway due to impaired cholesterol biosynthesis requires Ptch1/2
Carian Jägers, Henk Roelink
Dissecting signalling hierarchies in the patterning of the mouse primitive streak using micro-patterned EpiLC colonies
Jean-Louis Plouhinec, Mathieu Vieira, Gaël Simon, Jérôme Collignon, Benoit Sorre
A dynamic, spatially periodic, micro-pattern of HES5 underlies neurogenesis in the mouse spinal cord
V Biga, J Hawley, X Soto, E Johns, D Han, H Bennett, AD Adamson, J Kursawe, P Glendinning, C.S Manning, N Papalopulu
longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth
Scott Stewart, Heather K. Le Bleu, Gabriel A. Yette, Astra L. Henner, Amy E. Robbins, Joshua A. Braunstein, Kryn Stankunas
The Broad Role of Nkx3.2 in the Development of the Zebrafish Axial Skeleton
Laura Waldmann, Jake Leyhr, Hanqing Zhang, Caroline Öhman-Mägi, Amin Allalou, Tatjana Haitina
osr1 maintains renal progenitors and regulates podocyte development by promoting wnt2ba through antagonism of hand2
Bridgette E. Drummond, Brooke E. Chambers, Hannah M. Wesselman, Marisa N. Ulrich, Gary F. Gerlach, Paul T. Kroeger, Ignaty Leshchiner, Wolfram Goessling, Rebecca A. Wingert
Differential compartmentalization of BMP4/NOGGIN requires NOGGIN trans-epithelial transport
Tien Minh-Thuy Phan-Everson, Fred Etoc, Ali H Brivanlou, Eric D Siggia
Variability of an early developmental cell population underlies stochastic laterality defects
Roberto Moreno-Ayala, Pedro Olivares-Chauvet, Ronny Schäfer, Jan Philipp Junker
Valproic acid stimulates myogenesis in pluripotent stem cell–derived mesodermal progenitors in a Notch-dependent manner
Natacha Breuls, Nefele Giarratana, Laura Yedigaryan, Paolo Carai, Stephane Heymans, Adrian Ranga, Christophe M. Deroose, Maurilio Sampaolesi
Naa12 rescues embryonic lethality in Naa10-Deficient Mice in the amino-terminal acetylation pathway
Hyae Yon Kweon, Mi-Ni Lee, Max Dörfel, Seungwoon Seo, Leah Gottlieb, Thomas Papazyan, Nina McTiernan, Rasmus Ree, Andrew Garcia, Michael Flory, Jonathan Crain, Alison Sebold, Scott Lyons, Ahmed Ismail, Elaine Marchi, Seong-keun Sonn, Se-Jin Jeong, Sejin Jeon, Shinyeong Ju, Simon J. Conway, TaeSoo Kim, Hyun-Seok Kim, Cheolju Lee, Tae-Young Roh, Thomas Arnesen, Ronen Marmorstein, Gholson J. Lyon, Goo Taeg Oh
SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells
Romina J. Bevacqua, Jonathan Y. Lam, Heshan Peiris, Robert L. Whitener, Seokho Kim, Xueying Gu, Mollie S.H. Friedlander, Seung K. Kim
Lactate Accelerates Mouse ES Cell Differentiation Towards the XEN Lineage
Mohamed I. Gatie, Tyler T. Cooper, Gilles A. Lajoie, Gregory M. Kelly
ICM cells can be partitioned robustly through transient synchronization using secreted FGF4
Xiaochan Xu, Ala Trusina, Kim Sneppen
Association between erythrocyte dynamics and vessel remodelling in developmental vascular networks
Qi Zhou, Tijana Perovic, Ines Fechner, Lowell T. Edgar, Peter R. Hoskins, Holger Gerhardt, Timm Krüger, Miguel O. Bernabeu
Interneuron origins in the embryonic porcine medial ganglionic eminence
Mariana L. Casalia, Tina Li, Harrison Ramsay, Pablo J. Ross, Mercedes F. Paredes, Scott C. Baraban
MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis
Patrick A. Carroll, Pei Feng Cheng, Brian W Freie, Sivakanthan Kasinathan, Haiwei Gu, Theresa Hedrich, James A. Dowdle, Vivek Venkataramani, Vijay Ramani, Daniel Raftery, Jay Shendure, Donald E. Ayer, Charles H. Muller, Robert N. Eisenman
Neuroepithelial progenitors generate and propagate non-neuronal action potentials across the spinal cord
Kalaimakan Hervé Arulkandarajah, Guillaume Osterstock, Agathe Lafont, Hervé Le Corronc, Nathalie Escalas, Silvia Corsini, Barbara Le Bras, Juliette Boeri, Antonny Czarnecki, Christine Mouffle, Erika Bullier, Elim Hong, Cathy Soula, Pascal Legendre, Jean-Marie Mangin
Zfp36l1 and Zfp36l2 balances proliferation and differentiation in the developing retina
Fuguo Wu, Tadeusz Kaczynski, Louise S. Matheson, Tao Liu, Jie Wang, Martin Turner, Xiuqian Mu
DDI2 protease activity controls embryonic development and inflammation via TCF11/NRF1
Monika Siva, Stefanie Haberecht-Müller, Michaela Prochazkova, Jan Prochazka, Frantisek Sedlak, Kallayanee Chawengsaksophak, Petr Kasparek, Radislav Sedlacek, Jan Konvalinka, Elke Krüger, Klara Grantz Saskova
Muscle Van Gogh-like 2 shapes the neuromuscular synapse by regulating MuSK signaling activity
Myriam Boëx, Julien Messéant, Steve Cottin, Marius Halliez, Stéphanie Bauché, Céline Buon, Nathalie Sans, Mireille Montcouquiol, Jordi Molgó, Muriel Amar, Arnaud Ferry, Mégane Lemaitre, Andrée Rouche, Dominique Langui, Asha Baskaran, Bertrand Fontaine, Laure Strochlic
Fetal estrogens are not involved in sex determination but critical for early ovarian differentiation in rabbits
Geneviève Jolivet, Nathalie Daniel-Carlier, Erwana Harscoët, Eloïse Airaud, Aurélie Dewaele, Cloé Pierson, Frank Giton, Laurent Boulanger, Nathalie Daniel, Béatrice Mandon-Pépin, Maëlle Pannetier, Eric Pailhoux
Mechano-chemical feedback leads to competition for BMP signalling during pattern formation
Daniel J. Toddie-Moore, Martti P. Montanari, Ngan Vi Tran, Evgeniy M. Brik, Hanna Antson, Isaac Salazar-Ciudad, Osamu Shimmi
Lineage-specific control of convergent differentiation by a Forkhead repressor
Karolina Mizeracka, Julia M. Rogers, Jonathan D. Rumley, Shai Shaham, Martha L. Bulyk, John I. Murray, Maxwell G. Heiman
DAF-16/FoxO and DAF-12/VDR control cellular plasticity both cell-autonomously and via interorgan signaling
Ulkar Aghayeva, Abhishek Bhattacharya, Surojit Sural, Eliza Jaeger, Matthew Churgin, Christopher Fang-Yen, Oliver Hobert
Sustained expression of unc-4/Hox and unc-37/Groucho in postmitotic neurons specifies the spatial organization of the cholinergic synapses in C. elegans
Mizuki Kurashina, Jane Wang, Kathy Kyungeun Lee, Arpun Johal, Kota Mizumoto
Neuronal regulated Ire1-dependent mRNA decay controls germline differentiation in C. elegans
Mor Levi-Ferber, Rewayd Shalash, Adrien Le Thomas, Yehuda Salzberg, Maor Shurgi, Avi Ashkenazi, Sivan Henis-Korenblit
Functional analysis of caspase cleavable proteoforms from the Drosophila GSK-3 gene shaggy
Dagmara Korona, Daniel Nightingale, Bertrand Fabre, Michael Nelson, Bettina Fischer, Glynnis Johnson, Simon Hubbard, Kathryn Lilley, Steven Russell
Bab2 activates JNK signaling to reprogram Drosophila wing disc development
Yunpo Zhao, Jianli Duan, Alexis Dziedziech, Sabrina Büttner, Ylva Engström
Autonomous termination of proliferation in the Drosophila wing disc is TORC1 dependent
Katrin Strassburger, Marilena Lutz, Sandra Müller, Aurelio A. Teleman
JNK signaling in pioneer neurons directs the architectural organization of the CNS and coordinates the motor activity of the Drosophila embryo
Katerina Karkali, Timothy E. Saunders, Samuel W. Vernon, Richard A. Baines, George Panayotou, Enrique Martín-Blanco
Ecdysone coordinates plastic growth with robust pattern in the developing wing
André Nogueira Alves, Marisa Mateus Oliveira, Takashi Koyama, Alexander Shingleton, Christen Mirth
Scaling of Internal Organs during Drosophila Embryonic Development
P. Tiwari, H. Rengarajan, T. E. Saunders
The tolerance to hypoxia is defined by a time-sensitive response of the gene regulatory network in sea urchin embryos
Majed Layous, Lama Khalaily, Tsvia Gildor, Smadar Ben-Tabou de-Leon
Cellular and Developmental Basis of Avian Structural Coloration
Vinodkumar Saranathan, Cédric Finet
Wnt/β-Catenin Signaling Controls Spatio-Temporal Elasticity Patterns in Extracellular Matrix during Hydra Morphogenesis
Mariam Veschgini, Hendrik O Petersen, Fernanda F Rossetti, Wasim Abuillan, Stefan Kaufmann, Ryo Suzuki, Manfred Burghammer, Suat Özbek, Thomas W Holstein, Motomu Tanaka
Wnt3 expression as a readout of tissue stretching during Hydra regeneration
Jaroslav Ferenc, Panagiotis Papasaikas, Jacqueline Ferralli, Yukio Nakamura, Sebastien Smallwood, Charisios D. Tsiairis
Adaptive cell invasion maintains organ homeostasis
Julia Peloggia, Daniela Münch, Paloma Meneses-Giles, Andrés Romero-Carvajal, Melainia McClain, Y. Albert Pan, Tatjana Piotrowski
F-actin Re-organization Mediates Hierarchical Morphogenesis of Swallowtail Butterfly Wing Scale Nanostructures
Kwi Shan Seah, Vinodkumar Saranathan
The LINC complex transmits integrin-dependent tension to the nuclear lamina and represses epidermal differentiation
Emma Carley, Rachel K. Stewart, Abigail Zieman, Iman Jalilian, Diane. E. King, Amanda Zubek, Samantha Lin, Valerie Horsley, Megan C. King
Maternal vgll4a promotes blastoderm cohesion enabling yap1-mediated mechano-transduction during zebrafish epiboly
Carlos Camacho-Macorra, Noemí Tabanera, Paola Bovolenta, Marcos J Cardozo
Mechanical competition alters the cellular interpretation of an endogenous genetic programme
Sourabh Bhide, Denisa Gombalova, Gregor Mönke, Johannes Stegmaier, Valentyna Zinchenko, Anna Kreshuk, Julio M Belmonte, Maria Leptin
Deletion of INPP5E in the murine retina impairs axoneme formation and prevents photoreceptor disc morphogenesis
Ali S. Sharif, Cecilia D. Gerstner, Martha A. Cady, Vadim Y. Arshavsky, Christina Mitchell, Guoxin Ying, Jeanne M. Frederick, Wolfgang Baehr
Arrested coalescence of multicellular aggregates
David Oriola, Miquel Marin-Riera, Germaine Aalderink, Kerim Anlas, Nicola Gritti, James Sharpe, Vikas Trivedi
Axial Elongation of Caudalized Human Organoids Mimics Neural Tube Development
ARG Libby, DA Joy, NH Elder, EA Bulger, MZ Krakora, EA Gaylord, F Mendoza-Camacho, JC Butts, TC McDevitt
Somite surface tension buffers imprecise segment lengths to ensure left-right symmetry
Sundar R. Naganathan, Marko Popović, Andrew C. Oates
Short stop is a gatekeeper at the ring canals of Drosophila ovary
Wen Lu, Margot Lakonishok, Vladimir I. Gelfand
The EMT transcription factor Snai1 maintains myocardial wall integrity by repressing intermediate filament gene expression
Alessandra Gentile, Anabela Bensimon-Brito, Rashmi Priya, Hans-Martin Maischein, Janett Piesker, Stefan Günther, Felix Gunawan, Didier Y.R. Stainier
Aster repulsion drives local ordering in an active system
Jorge de-Carvalho, Sham Tlili, Lars Hufnagel, Timothy E. Saunders, Ivo A. Telley
Physics of blastocoel formation by hydro-osmotic lumen coarsening
Mathieu Le Verge–Serandour, Hervé Turlier
Vimentin provides target search efficiency and mechanical resilience for dendritic cell migration
Luiza Da Cunha Stankevicins, M. Reza Shaebani, Doriane Vesperini, Marta Urbanska, Daniel A. D. Flormann, Emmanuel Terriac, Annica K. B. Gad, Fang Cheng, John E. Eriksson, Franziska Lautenschläger
BAP1/ASXL complex modulation regulates Epithelial-Mesenchymal Transition during trophoblast differentiation and invasion
Vicente Perez-Garcia, Pablo Lopez-Jimenez, Graham J Burton, Ashley Moffett, Margherita Y. Turco, Myriam Hemberger
BBLN-1 is essential for intermediate filament organization and apical membrane morphology
Sanne Remmelzwaal, Florian Geisler, Riccardo Stucchi, Suzanne van der Horst, Milena Pasolli, Jason R. Kroll, Olga D. Jarosinska, Anna Akhmanova, Christine A. Richardson, Maarten Altelaar, Rudolf E. Leube, João J. Ramalho, Mike Boxem
Rapid assembly of a polar network architecture by formins downstream of RhoA pulses drives efficient cortical actomyosin contractility
Vlad Costache, Serena Prigent Garcia, Camille N. Plancke, Jing Li, Simon Begnaud, Shashi Kumar Suman, Taeyoon Kim, François B. Robin
A Genetic Screen for Temperature-sensitive Morphogenesis-defective Caenorhabditis elegans Mutants
Molly Christine Jud, Josh Lowry, Thalia Padilla, Erin Clifford, Yuqi Yang, Francesca Fennell, Alexander Miller, Danielle Hamill, Austin Harvey, Martha Avila-Zavala, Hong Shao, Nhah NguyenTran, Zhirong Bao, Bruce Bowerman
The Control of Lung Branching Morphogenesis
Dagmar Iber
| Genes & genomes
An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution
Aubrey G.A. Howard IV, Phillip A. Baker, Rodrigo Ibarra-García-Padilla, Joshua A. Moore, Lucia J. Rivas, James J. Tallman, Eileen W. Singleton, Jessa L. Westheimer, Julia A. Corteguera, Rosa A. Uribe
Single cell transcriptomics of the developing zebrafish lens and identification of putative controllers of lens development
Dylan Farnsworth, Mason Posner, Adam Miller
Single cell RNA analysis of trunk neural crest cells in zebrafish identifies pre-migratory populations expressing markers of differentiated derivatives
Ezra Lencer, Rytis Prekeris, Kristin Bruk Artinger
Diversity of developing peripheral glia revealed by single cell RNA sequencing
OE Tasdemir-Yilmaz, NR Druckenbrod, OO Olukoya, AR Yung, I Bastille, MF Pazyra-Murphy, A Sitko, EB Hale, S Vigneau, AA Gimelbrant, P Kharchenko, LV Goodrich, RA Segal
Resolving the transcriptional transitions associated with oligodendrocyte generation from adult neural stem cells by single cell sequencing
Kasum Azim, Filippo Calzolari, Martina Cantone, Rainer Akkermann, Julio Vera, Hans-Peter Hartung, Onur Basak, Arthur Morgan Butt, Patrick Küry
Single-Cell Atlas of Early Human Brain Development Highlights Heterogeneity of Human Neuroepithelial Cells and Early Radial Glia
Ugomma C. Eze, Aparna Bhaduri, Maximilian Haeussler, Tomasz J. Nowakowski, Arnold R. Kriegstein
Dissecting human skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses
Jian He, Jing Yan, Jianfang Wang, Liangyu Zhao, Qian Xin, Yang Zeng, Yuxi Sun, Han Zhang, Zhijie Bai, Zongcheng Li, Yanli Ni, Yandong Gong, Yunqiao Li, Han He, Zhilei Bian, Yu Lan, Chunyu Ma, Lihong Bian, Heng Zhu, Bing Liu, Rui Yue
Single cell multi-omic analysis identifies a Tbx1-dependent multilineage primed population in the murine cardiopharyngeal mesoderm
Hiroko Nomaru, Yang Liu, Christopher De Bono, Dario Righelli, Andrea Cirino, Wei Wang, Silvia E. Racedo, Anelisa G. Dantas, Chenleng Cai, Claudia Angelini, Lionel Christiaen, Robert G. Kelly, Antonio Baldini, Deyou Zheng, Bernice Morrow
Single cell transcriptomic analyses reveal the impact of bHLH factors ATOH7 and Neurog2 on human retinal organoid development
Xiangmei Zhang, Igor Mandric, Kevin H. Nguyen, Thao T. T. Nguyen, Matteo Pellegrini, James C. R. Grove, Steven Barnes, Xian-Jie Yang
Distinct expression of select and transcriptome-wide isolated 3’UTRs suggests critical roles in development and transition states
Shaoyi Ji, Ze Yang, Leonardi Gozali, Thomas Kenney, Arif Kocabas, Carolyn Jinsook Park, Mary Hynes
H3K4 trimethylation is required for postnatal pancreatic endocrine cell functional maturation
Stephanie A. Campbell, Jocelyn Bégin, Cassandra L. McDonald, Ben Vanderkruk, Tabea L. Stephan, Brad G. Hoffman
Epigenetic control of coordinated hematopoietic and cardiovascular development by Rnf2 in zebrafish
XX Peng, G Feng, YH Sun
Haploid mouse germ cell precursors from embryonic stem cells reveal Xist activation from a single X chromosome
Eishi Aizawa, Corinne Kaufmann, Sarah Sting, Remo Freimann, Anton Wutz
SPEN is Required for Xist Upregulation during Initiation of X Chromosome Inactivation
Teresa Robert-Finestra, Beatrice F. Tan, Hegias Mira-Bontenbal, Erika Timmers, Cristina Gontan-Pardo, Sarra Merzouk, Benedetto Daniele Giaimo, François Dossin, Wilfred F. J. van IJcken, John W. M. Martens, Tilman Borggrefe, Edith Heard, Joost Gribnau
Oct1 recruits the histone lysine demethylase Utx to canalize lineage specification
Jelena Perovanovic, Zuolian Shen, Yifan Wu, Dean Tantin
Histone H4K20 methylation synchronizes cytoskeletal dynamics with cell cycle phases during epidermal differentiation
Alessandro Angerilli, Janet Tait, Julian Berges, Irina Shcherbakova, Tamas Schauer, Pawel Smialowski, Ohnmar Hsam, Edith Mentele, Dario Nicetto, Ralph A.W. Rupp
Early cis-regulatory events in the formation of retinal horizontal cells
Estie Schick, Kevin C. Gonzalez, Pooja Dutta, Kazi Hossain, Miruna G. Ghinia Tegla, Mark M. Emerson
The comprehensive roadmaps of reprogramming and transformation unveiled antagonistic roles for bHLH transcription factors in the control of cellular plasticity
A. Huyghe, G. Furlan, J. Schroeder, J. Stüder, F. Mugnier, L. De Matteo, J. Wang, Y. Yu, N. Rama, B. Gibert, P. Wajda, I. Goddard, N. Gadot, M. Brevet, M. Siouda, P. Mulligan, R. Dante, P. Liu, H. Gronemeyer, M. Mendoza-Parra, J. Polo, F. Lavial
Chromatin remodeler Arid1a regulates subplate neuron identity and wiring of cortical connectivity
Daniel Z. Doyle, Mandy M. Lam, Adel Qalieh, Yaman Qalieh, Alice Sorel, Owen H. Funk, Kenneth Y. Kwan
Coordinated Changes in Gene Expression Kinetics Underlie both Mouse and Human Erythroid Maturation
Melania Barile, Ivan Imaz-Rosshandler, Isabella Inzani, Shila Ghazanfar, Jennifer Nichols, John C. Marioni, Carolina Guibentif, Berthold Göttgens
The transcription factor FoxO1 is required for the establishment of the human definitive endoderm
Joshua Nord, Daniel Schill, Kirthi Pulakanti, Sridhar Rao, Lisa Ann Cirillo
Pre-Implantation Alcohol Exposure Induces Lasting Sex-Specific DNA Methylation Programming Errors in the Developing Forebrain
LM Legault, K Doiron, M Breton-Larrivée, A Langford-Avelar, A Lemieux, M Caron, LA Jerome-Majewska, D Sinnett, S McGraw
AF10 (MLLT10) prevents somatic cell reprogramming through regulation of H3K79 methylation
Deniz Uğurlu-Çimen, Deniz Odluyurt, Kenan Sevinç, Nazlı Ezgi Özkan-Küçük, Burcu Özçimen, Deniz Demirtaş, Martin Philpott, Udo Oppermann, Nurhan Özlü, Tamer T. Önder
Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation
Jinyue Liao, Hoi Ching Suen, Alfred Chun Shui Luk, Tin-Lap Lee
Transcription-dependent spatial organization of a gene locus
Lev Barinov, Sergey Ryabichko, William Bialek, Thomas Gregor
The Nab2 RNA binding protein promotes sex-specific splicing of Sex lethal in Drosophila neuronal tissue
Binta Jalloh, J. Christopher Rounds, Brianna E. Brown, Isaac J. Kremsky, Ayan Banerjee, Derrick J. Morton, Rick S. Bienkowski, Milo B. Fasken, Anita H. Corbett, Kenneth H. Moberg
Low levels of Grainy head isoforms regulate Drosophila midgut intestinal stem cell differentiation
Nicole Dominado, Franca Casagranda, Nicole A. Siddall, Helen E. Abud, Gary R. Hime
Drosophila neural stem cells show a unique dynamic pattern of gene expression that is influenced by environmental factors
Alix Goupil, Carole Pennetier, Anthony Simon, Patricia Skorski, Allison Bardin, Renata Basto
Non-homologous end joining factors XLF, PAXX and DNA-PKcs support neural stem and progenitor cells development
Raquel Gago-Fuentes, Valentyn Oksenych
Neural stem cell interkinetic nuclear migration is controlled by a phosphatidylinositol transfer protein/non-canonical planar cell polarity signaling axis
Zhigang Xie, Vytas A. Bankaitis
Differential expression levels of Sox9 in early neocortical radial glial cells regulate the decision between stem cell maintenance and differentiation
Jaime Fabra-Beser, Jessica Alves Medeiros de Araujo, Diego Marques-Coelho, Loyal A. Goff, Ulrich Müller, Cristina Gil-Sanz
Coordinated regulation of ribosomes and proteasomes by PRMT1 in the maintenance of neural stemness of cancer cells and neural stem cells
Lu Chen, Min Zhang, Lei Fang, Xiaoli Yang, Liyang Xu, Lihua Shi, Ning Cao, Ying Cao
Dot1L interaction partner AF10 safeguards cell identity during the acquisition of pluripotency
Coral K. Wille, Edwin N. Neumann, Aniruddha J. Deshpande, Rupa Sridharan
Intermittent ERK oscillations downstream of FGF in mouse embryonic stem cells
Dhruv Raina, Fiorella Fabris, Luis G. Morelli, Christian Schröter
Capturing Human Trophoblast Development with Naïve Pluripotent Stem Cells In Vitro
Shingo Io, Mio Kabata, Yoshiki Iemura, Katsunori Semi, Nobuhiro Morone, Ikuhiro Okamoto, Tomonori Nakamura, Yoji Kojima, Chizuru Iwatani, Hideaki Tsuchiya, Belinda Kaswandy, Eiji Kondoh, Mitinori Saitou, Takuya Yamamoto, Masaki Mandai, Yasuhiro Takashima
Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors
Ying Li, Bhagirath Chaurasia, Vincent Kaddai, Joseph L. Wilkerson, J. Alan Maschek, James Cox, Peng Wei, Claire Bensard, Peter J Meikle, Hans Clevers, James A Shayman, Yoshio Hirabayashi, William L. Holland, Jared Rutter, Scott A. Summers
KLF17 promotes human naïve pluripotency but is not required for its establishment
Rebecca A. Lea, Afshan McCarthy, Stefan Boeing, Kathy K. Niakan
CTCF is a Barrier for Totipotent-like Reprogramming
Teresa Olbrich, Maria Vega-Sendino, Desiree Tillo, Wei Wu, Nicholas Zolnerowich, Andy D. Tran, Catherine N. Domingo, Mariajose Franco, Marta Markiewicz-Potoczny, Gianluca Pegoraro, Peter C. FitzGerald, Michael J. Kruhlak, Eros Lazzerini-Denchi, Elphege P. Nora, Andre Nussenzweig, Sergio Ruiz
Mouse embryonic stem cells switch migratory behaviour during early differentiation
Irene M. Aspalter, Wolfram Pönisch, Kevin J. Chalut, Ewa K. Paluch
De novo DNA methylation suppresses aberrant fate determination during pluripotency transition
Masaki Kinoshita, Meng Amy Li, Michael Barber, William Mansfield, Sabine Dietmann, Austin Smith
INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells
Hongyao Yu, Jiajia Wang, Brad Lackford, Brian Bennett, Jian-liang Li, Guang Hu
Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable?
Matheus P. Viana, Jianxu Chen, Theo A. Knijnenburg, Ritvik Vasan, Calysta Yan, Joy E. Arakaki, Matte Bailey, Ben Berry, Antoine Borensztejn, Jackson M. Brown, Sara Carlson, Julie A. Cass, Basudev Chaudhuri, Kimberly R. Cordes Metzler, Mackenzie E. Coston, Zach J. Crabtree, Steve Davidson, Colette M. DeLizo, Shailja Dhaka, Stephanie Q. Dinh, Thao P. Do, Justin Domingus, Rory M. Donovan-Maiye, Tyler J. Foster, Christopher L. Frick, Griffin Fujioka, Margaret A. Fuqua, Jamie L. Gehring, Kaytlyn A. Gerbin, Tanya Grancharova, Benjamin W. Gregor, Lisa Harrylock, Amanda Haupt, Melissa C. Hendershott, Caroline Hookway, Alan R. Horwitz, Chris Hughes, Eric J. Isaac, Gregory R. Johnson, Brian Kim, Andrew N. Leonard, Winnie Leung, Jordan J. Lucas, Susan A. Ludmann, Blair M. Lyons, Haseeb Malik, Ryan McGregor, Gabe E. Medrash, Sean L. Meharry, Kevin Mitcham, Irina A. Mueller, Timothy L. Murphy-Stevens, Aditya Nath, Angelique M. Nelson, Luana Paleologu, T. Alexander Popiel, Megan M. Riel-Mehan, Brock Roberts, Lisa M. Schaefbauer, Magdalena Schwarzl, Jamie Sherman, Sylvain Slaton, M. Filip Sluzewski, Jacqueline E. Smith, Youngmee Sul, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Daniel T. Toloudis, Andrew P. Tucker, Veronica Valencia, Winfried Wiegraebe, Thushara Wijeratna, Ruian Yang, Rebecca J. Zaunbrecher, Allen Institute for Cell Science, Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski
SUMO maintains the chromatin environment of human induced pluripotent stem cells
Barbara Mojsa, Michael H. Tatham, Lindsay Davidson, Magda Liczmanska, Jane E. Wright, Nicola Wiechens, Marek Gierlinski, Tom Owen-Hughes, Ronald T. Hay
Dynamic erasure of X chromosome upregulation during iPSC reprogramming and in the inner cell mass
D Chandel, C H Naik, S Gayen
Sestrins regulate age-induced deterioration of muscle stem cell homeostasis
Benjamin A. Yang, Jesus Castor-Macias, Paula Fraczek, Lemuel A. Brown, Myungjin Kim, Susan V. Brooks, Jun Hee Lee, Carlos A. Aguilar
Characterization of human embryonic stem cells in animal component-free medium
Masakazu Machida, Rie Abutani, Hiroshi Miyajima, Tetsuji Sasaki, Yoshiko Abe, Hidenori Akutsu, Akihiro Umezawa
Direct differentiation of Dental Pulp Pluripotent-like Stem Cells differentiation into Hepatocyte-like Cells
Carlos Gil-Recio, Sheyla Montori, Cámara Vallejo, Saddam Al Demour, E. Ferrés-Padró, Miguel Barajas, Carles Martin, Ashraf Al Madhoun, Maher Atari
Transcription factor network analysis identifies REST/NRSF as an intrinsic regulator of CNS regeneration
Yuyan Cheng, Yuqin Yin, Alice Zhang, Alexander M. Bernstein, Riki Kawaguchi, Kun Gao, Kyra Potter, Hui-Ya Gilbert, Yan Ao, Jing Ou, Catherine J. Fricano-Kugler, Jeffrey L. Goldberg, Clifford J. Woolf, Michael V. Sofroniew, Larry I. Benowitz, Daniel H. Geschwind
Dynamics and variability of neuronal subtype responses during growth, degrowth, and regeneration
Jamie A. Havrilak, Layla Al-Shaer, Noor Baban, Nesli Akinci, Michael J. Layden
Decellularization enables functional analysis of ECM remodeling in planarian regeneration
Ekasit Sonpho, Frederick G. Mann Jr., Michaella Levy, Eric J. Ross, Carlos Guerrero-Hernández, Laurence Florens, Anita Saraf, Viraj Doddihal, Puey Ounjai, Alejandro Sánchez Alvarado
Apoptosis is a generator of Wnt-dependent regeneration and homeostatic cell renewal in the ascidian Ciona
William R. Jeffery, Spela Goricki
Critical role for astrocyte NAD+ glycohydrolase in myelin injury and regeneration
Monica R. Langley, Chan-Il Choi, Thais R. Peclat, Yong Guo, Whitney Simon, Hyesook Yoon, Laurel Kleppe, Claudia F. Lucchinetti, Claudia C.S. Chini, Eduardo N. Chini, Isobel A. Scarisbrick
Robo2 drives target selective peripheral nerve regeneration in response to glia derived signals
Patricia L. Murphy, Jesse Isaacman-Beck, Michael Granato
Transformed notochordal cells trigger chronic wounds destabilizing the vertebral column and bone homeostasis
Paco Lopez-Cuevas, Luke Deane, Yushi Yang, Chrissy L Hammond, Erika Kague
16p12.1 deletion orthologs are expressed in motile neural crest cells and are important for regulating craniofacial development in Xenopus laevis
Micaela Lasser, Jessica Bolduc, Luke Murphy, Caroline O’Brien, Sangmook Lee, Santhosh Girirajan, Laura Anne Lowery
Computational profiling of hiPSC-derived heart organoids reveals chamber defects associated with Ebstein’s anomaly
Wei Feng, Hannah Schriever, Shan Jiang, Abha Bais, Dennis Kostka, Guang Li
A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation
Jiayang Chen, Mary E. Lambo, Xia Ge, Joshua T. Dearborn, Yating Liu, Katherine B. McCullough, Raylynn G. Swift, Dora R. Tabachnick, Lucy Tian, Kevin Noguchi, Joel R. Garbow, Harrison W. Gabel, Keith B. Hengen, Susan E. Maloney, Joseph D. Dougherty
Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19
Courtney Tindle, MacKenzie Fuller, Ayden Fonseca, Sahar Taheri, Stella-Rita Ibeawuchi, Nathan Beutler, Amanraj Claire, Vanessa Castillo, Moises Hernandez, Hana Russo, Jason Duran, Laura E. Crotty Alexander, Ann Tipps, Grace Lin, Patricia A. Thistlethwaite, Ranajoy Chattopadhyay, Thomas F. Rogers, Debashis Sahoo, Pradipta Ghosh, Soumita Das
Neural stem cells restore motor and cognitive function in a macaque model of Parkinson′s disease
Florence Wianny, Kwamivi Dzahini, Karim Fifel, Charles R.E. Wilson, Agnieszka Bernat, Virginie Dolmazon, Pierre Misery, Camille Lamy, Howard M. Cooper, Emmanuel Procyk, Henry Kennedy, Pierre Savatier, Colette Dehay, Julien Vezoli
Differences in neuronal numbers, morphology and developmental apoptosis in mice nigra provide experimental evidence of ontogenic origin of vulnerability to Parkinson’s disease
D J Vidyadhara, Haorei Yarreiphang, Trichur R Raju, Phalguni Anand Alladi
A novel RLIM/RNF12 variant disrupts protein stability and function to cause severe Tonne-Kalscheuer syndrome
Francisco Bustos, Carmen Espejo-Serrano, Anna Segarra-Fas, Alison J. Eaton, Kristin D. Kernohan, Meredith J. Wilson, Lisa G. Riley, Greg M. Findlay
Abnormal AMPAR-mediated synaptic plasticity, cognitive and autistic-like behaviors in a missense Fmr1 mutant mouse model of Fragile X syndrome
Marta Prieto, Alessandra Folci, Gwénola Poupon, Sara Schiavi, Valeria Buzzelli, Marie Pronot, Urielle François, Paula Pousinha, Norma Lattuada, Sophie Abelanet, Sara Castagnola, Magda Chafai, Anouar Khayachi, Carole Gwizdek, Frédéric Brau, Emmanuel Deval, Maura Francolini, Barbara Bardoni, Yann Humeau, Viviana Trezza, Stéphane Martin
Grb10a knockdown in Danio rerio during early life alters growth and cardiometabolic function associated with a remodelled transcriptome
Bridget L Evans, Terence Garner, Chiara De Leonibus, Oliver H Wearing, Holly A Shiels, Adam F L Hurlstone, Peter E Clayton, Adam Stevens
Ste20-like kinase is critical for inhibitory synapse maintenance and its deficiency confers a developmental dendritopathy
Susanne Schoch, Anne Quatraccioni, Barbara K. Robens, Robert Maresch, Karen M.J. van Loo, Tony Kelly, Thoralf Opitz, Valeri Borger, Dirk Dietrich, Julika Pitsch, Heinz Beck, Albert J. Becker
Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium
Alon Israeli, Yogev Burko, Sharona Shleizer-Burko, Iris Daphne Zelnik, Noa Sela, Mohammad R. Hajirezaei, Alisdair R. Fernie, Takayuki Tohge, Naomi Ori, Maya Bar
Cortical microtubule remodelling during strigolactone- and light-mediated growth inhibition of Arabidopsis hypocotyls
Yuliya A. Krasylenko, George Komis, Sonya Hlynska, Tereza Vavrdová, Miroslav Ovečka, Tomáš Pospíšil, Jozef Šamaj
The Arabidopsis TTL3 protein interconnects brassinosteroid signalling and cytoskeleton during lateral root development
Pengfei Xin, Jakub Schier, Ivan Kulich, Joseph G. Dubrovsky, Vielle-Calzada Jean-Philippe, Aleš Soukup
Hexose fluxes, mediated by vacuolar SWEET transporters, are important for xylem development in the inflorescence stem of Arabidopsis thaliana
Emilie Aubry, Beate Hoffmann, Françoise Vilaine, Françoise Gilard, Patrick A.W. Klemens, Florence Guérard, Bertrand Gakière, H. Ekkehard Neuhaus, Catherine Bellini, Sylvie Dinant, Rozenn Le Hir
Root electrotropism in Arabidopsis does not depend on auxin distribution, requires cytokinin and follows a power-law response curve
Nicholas Oliver, Maddalena Salvalaio, Deniz Tiknaz, Maximillian Schwarze, Nicolas Kral, Soo-Jeong Kim, Giovanni Sena
Independent parental contributions initiate zygote polarization in Arabidopsis thaliana
Kai Wang, Houming Chen, Yingjing Miao, Yanfei Ma, Agnes Henschen, Jan U. Lohmann, Sascha Laubinger, Martin Bayer
Comparative Analysis of Embryo Proper and Suspensor Transcriptomes in Plant Embryos With Different Morphologies
Min Chen, Jer-Young Lin, Xiaomeng Wu, Nestor R. Apuya, Kelli F. Henry, Brandon H. Le, Anhthu Q. Bui, Julie M. Pelletier, Shawn Cokus, Matteo Pellegrini, John J. Harada, Robert B. Goldberg
A gene regulatory network critical for axillary bud dormancy directly controlled by Arabidopsis BRANCHED1
Sam W. van Es, Aitor Muñoz-Gasca, Francisco J. Romero-Campero, Eduardo González-Grandío, Pedro de los Reyes, Carlos Tarancón, Aalt D.J. van Dijk, Wilma van Esse, Gerco C. Angenent, Richard Immink, Pilar Cubas
Shoot-root interaction in control of camalexin exudation in Arabidopsis
Anna Koprivova, Vanessa Volz, Stanislav Kopriva
Organ geometry channels cell fate in the Arabidopsis ovule primordium
Elvira Hernandez-Lagana, Gabriella Mosca, Ethel Mendocilla Sato, Nuno Pires, Anja Frey, Alejandro Giraldo-Fonseca, Ueli Grossniklaus, Olivier Hamant, Christophe Godin, Arezki Boudaoud, Daniel Grimanelli, Daphné Autran, Célia Baroux
AINTEGUMENTA and AINTEGUMENTA-LIKE6 directly regulate floral homeotic and growth genes in young flowers
Beth A. Krizek, Alexis T. Bantle, Jorman M. Heflin, Han Han, Nowlan H. Freese, Ann E. Loraine
The SYP123-VAMP727 SNARE complex is involved in the delivery of inner cell wall components to the root hair shank in Arabidopsis
Tomoko Hirano, Kazuo Ebine, Takashi Ueda, Takumi Higaki, Takahiro Nakayama, Hiroki Konno, Hisako Takigawa-Imamura, Masa H. Sato
Blocking plasmodesmata in specific phloem cell types reduces axillary bud growth in Arabidopsis thaliana
Andrea Paterlini, Delfi Dorussen, Franziska Fichtner, Martin van Rongen, Ruth Delacruz, Ana Vojnović, Yrjö Helariutta, Ottoline Leyser
Integration of Cell Growth and Asymmetric Division During Lateral Root Initiation In Arabidopsis thaliana
Lilli Marie Schütz, Marion Louveaux, Amaya Vilches Barro, Sami Bouziri, Lorenzo Cerrone, Adrian Wolny, Anna Kreshuk, Fred A. Hamprecht, Alexis Maizel
A novel family of secreted insect proteins linked to plant gall development
Aishwarya Korgaonkar, Clair Han, Andrew L. Lemire, Igor Siwanowicz, Djawed Bennouna, Rachel Kopec, Peter Andolfatto, Shuji Shigenobu, David L. Stern
Enhanced reproductive thermotolerance is associated with increased accumulation of flavonols in pollen of the tomato high-pigment 2 mutant
Nicolas Rutley, Golan Miller, Fengde Wang, Jeffrey F Harper, Gad Miller, Michal Lieberman Lazarovich
The SINGLE FLOWER (SFL) gene encodes a MYB transcription factor that regulates the number of flowers produced by the inflorescence of chickpea
Cristina Caballo, Ana Berbel, Raul Ortega, Juan Gil, Teresa Millán, Josefa Rubio, Francisco Madueño
Characterization of the single FERONIA homolog in Marchantia polymorpha reveals an ancestral role of CrRLK1L receptor kinases in regulating cell expansion and morphological integrity
Martin A. Mecchia, Moritz Rövekamp, Alejandro Giraldo-Fonseca, Dario Meier, Philippe Gadient, John L. Bowman, Ueli Grossniklaus
Interactions Between SQUAMOSA and SVP MADS-box Proteins Regulate Meristem Transitions During Wheat Spike Development
Kun Li, Juan M. Debernardi, Chengxia Li, Huiqiong Lin, Chaozhong Zhang, Jorge Dubcovsky
Nodal root diameter and node number in maize (Zea mays L.) interact to influence plant growth under nitrogen stress
Hannah M. Schneider, Jennifer T. Yang, Kathleen M. Brown, Jonathan P. Lynch
Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability.
JF McKenna, HK Gumber, ZM Turpin, AM Jalovec, AC Kartick, K Graumann, HW Bass
Mutation of the nuclear pore complex component, aladin1, disrupts asymmetric cell division in Zea mays (maize)
Norman B. Best, Charles Addo-Quaye, Bong-Suk Kim, Clifford F. Weil, Burkhard Schulz, Guri Johal, Brian P. Dilkes
Ribosome profiling elucidates the contribution of differential translation to differential gene expression in bundle sheath and mesophyll cells in maize
Prakitchai Chotewutmontri, Alice Barkan
Regulation of the plastochron by three MANY-NODED DWARF genes in barley
Ken-ichiro Hibara, Masayuki Miya, Sean Akira Benvenuto, Naoko Hibara-Matsuo, Manaki Mimura, Takanori Yoshikawa, Masaharu Suzuki, Makoto Kusaba, Shin Taketa, Jun-ichi Itoh
Control of the Azolla symbiosis sexual reproduction: ferns to shed light on the origin of floral regulation?
Laura W. Dijkhuizen, Badraldin Ebrahim Sayed Tabatabaei, Paul Brouwer, Niels Rijken, Valerie A. Buijs, Erbil Güngör, Henriette Schluepmann
A molecular toolkit for the green seaweed Ulva mutabilis
Jonas Blomme, Xiaojie Liu, Thomas B. Jacobs, Olivier De Clerck
Evolution of lbx spinal cord expression and function
José L. Juárez-Morales, Frida Weierud, Samantha England, Celia Denby, Nicole Santos, Sylvie Mazan, Katharine E. Lewis
From egg to adult: a developmental table of the ant Monomorium pharaonis
Luigi Pontieri, Arjuna Rajakumar, Ab Matteen Rafiqi, Rasmus Stenbak Larsen, Ehab Abouheif, Guojie Zhang
Hidden limbs in the “limbless skink” Brachymeles lukbani: developmental observations
Daniel Smith-Paredes, Oliver Griffith, Matteo Fabbri, Laurel Yohe, Daniel G. Blackburn, Cameron D. Siler, Bhart-Anjan S. Bhullar, Günter P. Wagner
Decidual cell differentiation is evolutionarily derived from fibroblast activation
Longjun Wu, Daniel J Stadtmauer, Jamie Maziarz, Gunter Wagner
Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing
Jason S Presnell, William E Browne
Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution
Spenser S. Smith, Daniel Chu, Tiange Qu, Richard A. Schneider
The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
Jialin Liu, Rebecca R. Viales, Pierre Khoueiry, James P. Reddington, Charles Girardot, Eileen E. M. Furlong, Marc Robinson-Rechavi
Baby makes three: maternal, paternal, and zygotic genetic effects shape larval phenotypic evolution
Christina Zakas, Matthew V. Rockman
Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity
Rachel A. Johnston, Philippe Vullioud, Jack Thorley, Henry Kirveslahti, Leyao Shen, Sayan Mukherjee, Courtney Karner, Tim Clutton-Brock, Jenny Tung
Gene family evolution underlies cell type diversification in the hypothalamus of teleosts
Maxwell E.R. Shafer, Ahilya N. Sawh, Alexander F. Schier
Dog color patterns explained by modular promoters of ancient canid origin
Danika L. Bannasch, Christopher B. Kaelin, Anna Letko, Robert Loechel, Petra Hug, Vidhya Jagannathan, Jan Henkel, Petra Roosje, Marjo K. Hytönen, Hannes Lohi, Meharji Arumilli, DoGA consortium, Katie M. Minor, James R. Mickelson, Cord Drögemüller, Gregory S. Barsh, Tosso Leeb
Global Age-Specific Patterns of Cyclic Gene Expression Revealed by Tunicate Transcriptome Atlas
Yotam Voskoboynik, Aidan Glina, Mark Kowarsky, Chiara Anselmi, Norma F Neff, Katherine J Ishizuka, Karla J Palmeri, Benyamin Rosental, Tal Gordon, Stephen R Quake, Irving L Weissman, Rachel Ben-Shlomo, Debashis Sahoo, Ayelet Voskoboynik
Asymmetric chromatin capture and nuclear envelopes separate endogenous and ectopic chromosomes after induced cell fusion
Bharath Sunchu, Nicole Lee, Roberto Carlos Segura, Clemens Cabernard
The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles
Sónia Gomes Pereira, Ana Laura Sousa, Catarina Nabais, Tiago Paixão, Alexander J. Holmes, Martin Schorb, Gohta Goshima, Erin M. Tranfield, Jörg D. Becker, Mónica Bettencourt-Dias
IFT88 transports Gucy2d, a guanylyl cyclase, to maintain sensory cilia function in Drosophila
Sascha Werner, Sihem Zitouni, Pilar Okenve-Ramos, Susana Mendonça, Anje Sporbert, Christian Spalthoff, Martin C. Göpfert, Swadhin Chandra Jana, Mónica Bettencourt-Dias
Plk4 triggers autonomous de novo centriole biogenesis and maturation
Catarina Nabais, Delphine Pessoa, Jorge de-Carvalho, Thomas van Zanten, Paulo Duarte, Satyajit Mayor, Jorge Carneiro, Ivo A. Telley, Mónica Bettencourt-Dias
Novel roles for BicD in pronuclear fusion and meiosis II progression via localization of the CHC/TACC/Msps complex to MII spindles
Paula Vazquez-Pianzola, Dirk Beuchle, Gabriela Saro, Greco Hernández, Giovanna Maldonado, Dominique Brunßen, Peter Meister, Beat Suter
Cytoplasmic Microtubule Organizing Centers Regulate Meiotic Spindle Positioning in Mouse Oocyte
Daniela Londono Vasquez, Katherine Rodriguez-Lukey, Susanta K. Behura, Ahmed Z. Balboula
A small increase in CHEK1 activity leads to the arrest of the first zygotic division in human
Beili Chen, Jianying Guo, Ting Wang, Qianhui Lee, Jia Ming, Fangfang Ding, Haitao Li, Zhiguo Zhang, Lin Li, Yunxia Cao, Jie Na
BUB-1 targets PP2A:B56 to regulate chromosome congression during meiosis I in C. elegans oocytes
Laura Bel Borja, Flavie Soubigou, Samuel J.P. Taylor, Conchita Fraguas Bringas, Jacqueline Budrewicz, Pablo Lara-Gonzalez, Christopher G. Sorensen Turpin, Joshua N. Bembenek, Dhanya K. Cheerambathur, Federico Pelisch
Lamin regulates the dietary restriction response via the mTOR pathway in Caenorhabditis elegans
Chayki Charar, Sally Metsuyanim-Cohen, Yosef Gruenbaum, Daniel Z Bar
A WDR35-dependent coatomer transports ciliary membrane proteins from the Golgi to the cilia
Tooba Quidwai, Emma A. Hall, Margaret A. Keighren, Weihua Leng, Petra Kiesel, Jonathan N. Wells, Laura C. Murphy, Joseph A. Marsh, Gaia Pigino, Pleasantine Mill
Cell patterning by secretion-induced plasma membrane flows
Veneta Gerganova, Iker Lamas, David M. Rutkowski, Aleksandar Vještica, Daniela Gallo Castro, Vincent Vincenzetti, Dimitrios Vavylonis, Sophie G Martin
Centrosome-dependent microtubule organization sets the conditions for axon formation
Durga Praveen Meka, Oliver Kobler, Souhaila Wuesthoff, Birgit Schwanke, Christoph Krisp, Nessa Schmuelling, René Rueter, Tabitha Ruecker, Hartmut Schlüter, Eugenio F. Fornasiero, Froylan Calderon de Anda
Dynamic positioning and precision of bistable gene expression boundaries through diffusion and morphogen decay
Melinda Liu Perkins
Shaping the Epigenetic Landscape: Complexities and Consequences
Megan A. Coomer, Lucy Ham, Michael P. H. Stumpf
Time and Space in Segmentation
Erik Clark
The role of mechanical interactions in EMT
Ryan J. Murphy, Pascal R. Buenzli, Tamara A. Tambyah, Erik W. Thompson, Honor J. Hugo, Ruth E. Baker, Matthew J. Simpson
Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions
Lisa Van den Broeck, Ryan J. Spurney, Adam P. Fisher, Michael Schwartz, Natalie M. Clark, Thomas T. Nguyen, Imani Madison, Mariah Gobble, Terri Long, Rosangela Sozzani
The basal level of gene expression associated with chromatin loosening shapes Waddington landscapes and controls cell differentiation
Gilles Flouriot, Charly Jehanno, Yann Le Page, Pascale Le Goff, Benjamin Boutin, Denis Michel
CeLaVi: An Interactive Cell Lineage Visualisation Tool
Irepan Salvador-Martínez, Marco Grillo, Michalis Averof, Maximilian J. Telford
Integrating central and peripheral neurons in elongating multi-lineage-organized gastruloids
Zachary T. Olmsted, Janet L. Paluh
Precise base editing for the in vivo study of developmental signaling and human pathologies in zebrafish
Marion Rosello, Juliette Vougny, François Czarny, Maria Caterina Mione, Jean-Paul Concordet, Shahad Albadri, Filippo Del Bene
Whole-organism eQTL mapping at cellular resolution with single-cell sequencing
Eyal Ben-David, James Boocock, Longhua Guo, Stefan Zdraljevic, Joshua S. Bloom, Leonid Kruglyak
Dynamics of myogenic differentiation using a novel Myogenin knock-in reporter mouse
Maria Benavente-Diaz, Glenda Comai, Daniela Di Girolamo, Francina Langa, Shahragim Tajbakhsh
Generation of a new Tbx6-inducible reporter mouse line to trace presomitic mesoderm derivatives throughout development and in adults
Laurent Yvernogeau, Anna Klaus, Carina van Rooijen, Catherine Robin
Tissue-specific transcription factor target identification in the Caenorhabditis elegans epidermis using targeted DamID
Dimitris Katsanos, Michalis Barkoulas
Molecular topography of an entire nervous system
Seth R Taylor, Gabriel Santpere, Alexis Weinreb, Alec Barrett, Molly B. Reilly, Chuan Xu, Erdem Varol, Panos Oikonomou, Lori Glenwinkel, Rebecca McWhirter, Abigail Poff, Manasa Basavaraju, Ibnul Rafi, Eviatar Yemini, Steven J Cook, Alexander Abrams, Berta Vidal, Cyril Cros, Saeed Tavazoie, Nenad Sestan, Marc Hammarlund, Oliver Hobert, David M. Miller III
Engineered Tissue Interfaces for in vitro and in vivo Regeneration
Ryan J. Hickey, Maxime Leblanc Latour, James L. Harden, Andrew E. Pelling
Functional tagging of endogenous proteins and rapid selection of cell pools (Rapid generation of endogenously tagged piwi in ovarian somatic sheath cells.)
Celine Marlin Andrews, Parthena Konstantinidou, Pavol Genzor, Daniel Stoyko, Alexandra R. Elchert, Leif Benner, Sushil Sobti, Esther Y. Katz, Qingcai Meng, Astrid D. Haase
X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs
Keith E Duncan, Kirk J Czymmek, Ni Jiang, August C. Thies, Christopher N. Topp
CellExplorer: a graphical user interface and a standardized pipeline for visualizing and characterizing single neurons
Peter C. Petersen, Joshua H. Siegle, Nicholas A. Steinmetz, Sara Mahallati, György Buzsáki
Engineering large chromosomal deletions by CRISPR-Cas9
Thomas F. Eleveld, Chaimaa Bakali, Paul P. Eijk, Phylicia Stathi, Pino J Poddighe, Bauke Ylstra
ZeBraInspector, a platform for the automated segmentation and analysis of body and brain volumes in whole 5 dpf zebrafish following simultaneous visualization with identical orientations
Sylvain Lempereur, Matthieu Simion, Elodie Machado, Fabrice Licata, Lilian Buzer, Isabelle Robineau, Julien Hémon, Payel Banerjee, Noémie De Crozé, Marc Léonard, Pierre Affaticati, Arnim Jenett, Hugues Talbot, Jean-Stéphane Joly
A versatile automated high-throughput drug screening platform for zebrafish embryos
Alexandra Lubin, Jason Otterstrom, Yvette Hoade, Ivana Bjedov, Eleanor Stead, Matthew Whelan, Gaia Gestri, Yael Paran, Elspeth Payne
MAPPER: A new image analysis pipeline unmasks differential regulation of Drosophila wing features
Nilay Kumar, Francisco Huizar, Trent Robinett, Keity J. Farfán-Pira, Dharsan Soundarrajan, Maria Unger, Pavel Brodskiy, Marcos Nahmad, Jeremiah J. Zartman
Automated hiPSC culture and sample preparation for 3D live cell microscopy
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Posted by Natalia Sanchez-Soriano, on 6 January 2021
Closing Date: 15 March 2021
We live in an ageing society with high incidence of cognitive, sensory and motor decline, as well as neurodegenerative diseases such as Alzheimer’s disease (AD) or Fronto-temporal Dementia (FTD). Although decay of synaptic functions is a clear hallmark of the aforementioned conditions, we know too little about the underlying causes. The overarching aim of this project is to study roles of the ageing- and neurodegenerative disease-related factor Tau during the regulation of synapses in health, ageing and disease.
Synapses are specialised neuronal cell junctions which contain complex machinery for rapid transmission of signals to partner cells. This machinery is frequently disrupted during ageing and in neurodegeneration and the resulting synaptic malfunction is an important cause for cognitive, sensory and motor decline. The underpinning mechanisms are poorly understood. To bridge this knowledge gap, we focus on Tau. Tau plays a vital role in the pathogenesis of neurodegenerative disorders and is also linked to physiological ageing. Accordingly, Tau is an important therapeutic target for the development of treatments of AD and FTD.
Considering Tau’s crucial roles during pathogenesis and treatment of dementia, it is vital to understand its physiological function. Tau loss is known to lead to age-related synaptic deficits both in mice and the fruit fly Drosophila, and our work has started to deliver first explanations. Thus, we have shown that Tau loss triggers aberrations of microtubule networks and axonal transport deficits affecting synapse formation and maintenance (Voelzmann et al., 2016, eLife 5, e14694ff.; Hahn et al., 2020, bioRxiv 2020.08.19.257808ff.). We now find from our proteomic and preliminary functional studies that Tau plays even more direct roles by binding to factors that are important for synaptic function. The aim of this project is to understand these synaptic mechanisms of Tau. For this, we will use the model organism Drosophila which harbours Tau and synaptic machinery that is well conserved with humans, but can be studied far more effectively than in other model organisms. Using Drosophila‘s efficient genetics, powerful experimental strategies and simple robust behavioural assays, you will study the functional links between Tau and its synaptic binding partners. This will involve inter-disciplinary approaches using genetics, molecular biology, biochemistry, cell biology, cell culture and in vivo studies, cutting-edge bioimaging of synaptic activity and behavioural studies. You will unravel mechanisms of Tau at synapses as a means to understand neuronal decay during ageing and in neurodegeneration.
Applications from candidates, ideally with some background in cell biology, genetics, neuroscience and/or biomedical sciences are encouraged to apply. The successful applicant will be based in the Institute of Systems, Molecular & Integrative Biology, University of Liverpool, supervised by Dr Sánchez-Soriano (https://sanchezlab.wordpress.com/research/), whilst working closely with Dr Olena Riabinina (http://insectneurolab.com/) at the Department of Biosciences, Durham University. Interested applicants should contact Dr Sanchez-Soriano to discuss the project: n.sanchez-soriano@liverpool.ac.uk.
Application deadline: 22 January
For more information on how to apply:
https://www.nld-dtp.org.uk/how-apply
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Posted by Daniel Suter, on 5 January 2021
Closing Date: 15 March 2021
A postdoctoral research associate position is available immediately to investigate the role of reactive oxygen species (ROS) as physiological signaling molecules in axonal growth and guidance in the lab of Dr. Daniel M. Suter at Purdue University, West Lafayette, IN https://suterlab.bio.purdue.edu/. Specifically, the work will investigate the molecular and cellular mechanisms of how ROS regulate axonal growth and guidance in vitro and in vivo. The successful applicant has experience in cell biology and molecular biology. Additional expertise in developmental neuroscience, microscopy, and working with zebrafish is desirable but not required. This position is supported through funding from the NIH.
Highly motivated candidates with a PhD in cell biology, molecular biology, or neuroscience who are interested to participate in this exciting project at the interface of cellular and developmental neurobiology are invited to send their CV, a brief statement of research interests and contact information of three referees to Dr. Suter.
Dr. Daniel M. Suter
Department of Biological Sciences
Purdue University
915 West State Street
West Lafayette, IN 47907
USA
dsuter@purdue.edu
765-496-1562
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Posted by Gaelle Recher, on 5 January 2021
Closing Date: 15 March 2021
The BiOf lab http://biof-lab.org/ has developed a microfluidic technique, the Cellular Capsules Technology, that allows them to produce multicellular spheroids and organoids in a high throughput and controlled format. The applications in tissue engineering, oncology and regenerative medicine and toxicology testing are numerous. The recruited postdocs will be involved in the interdisciplinary projects pursued by the team in engineering multiscale vascularized tissues, reconstructing a functional liver lobule, deciphering the impact of mechanical cues on hepatocarcinoma and glioblastoma progression in vitro models, developing innovative microscopy techniques for thick tissue imaging.
We seek for talented scientists with exceptional motivation and outstanding expertise (i.e. PhD) in biophotonics /image analysis, cancer or stem cell biology, microfluidics, biophysics or tissue engineering.
The proposed funding is for 12 months and can be renewed up to 36 months. The salary will be adapted to the experience of the applicant. Starting date will be between March and June 2021.
Applicants should email curriculum vitae, statement of research interests and at least two recommendation letters to Gaëlle Recher (gaelle.recher@institutoptique.fr) and Pierre Nassoy (pierre.nassoy@u-bordeaux.fr).
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Posted by Kristen Panfilio, on 4 January 2021
Closing Date: 15 March 2021
A postdoctoral research position is available in the group of Dr. Kristen Panfilio at the University of Warwick, UK, to join our BBSRC-funded project on how polyploid nuclear structure influences cellular function in dynamic epithelial tissues. This is a full-time, fixed-term position for up to 36 months, integrating developmental biology, bioinformatics, cell cycle regulation, genome organization, and 4D live cell imaging.
Polyploidy is hypothesized to aid epithelial barrier formation and its repair after wounding and to rapidly supply gene products by transcription from multiple gene copies. Yet polyploid genomic structure may be unstable and require active inhibition of apoptosis through regulatory processes that are not yet well understood. Investigating the costs and benefits of polyploidy is essential to understand tissue-specific development, homeostasis, and ageing.
The two extraembryonic tissues of insects offer an excellent – and inherently comparative – research model, spanning key developmental stages for morphogenesis and cellular physiology. Our research species is the flour beetle Tribolium castaneum, which offers advanced genetic resources and where we integrate fluorescent live cell imaging and next-generation sequencing approaches (see the lab’s recent publications in eLife 5:e13834, Development 143:3002, Commun. Biol. 3:552). The project uses methods to assess nuclear size and tissue integrity, quantify gene expression, and genetically challenge barrier organization and cell number. Altogether, we will test long-standing hypotheses on polyploidy function and its end-stage implications in animal tissues. A complete description of the project is available at: https://gtr.ukri.org/projects?ref=BB%2FV002392%2F1.
You will have a Ph.D. or equivalent and good knowledge and experience in genetics, cell and developmental biology, standard molecular biology techniques,and working with NGS data, as evidenced by your Ph.D. thesis and/or authored papers in peer-reviewed journals. Familiarity with the fields of insect developmental genetics and comparative genomics would also be highly advantageous. Practical experience in any of the following is desired: advanced microscopy (including light sheet fluorescence microscopy),RNAi, FACS, RT-qPCR, and computational work with either sequencing or imaging data. We will provide full training in new techniques, supported by the possibility for international travel and collaboration.
Enquiries and expressions of interest directly to Kristen (K.Panfilio@warwick.ac.uk) are welcome, with applications made on-line (post number 103508). Full applications will include contact details for at least two referees, a CV, and covering letter stating why you are interested in the topic and what you would bring to the project. The application closing date is 7th February 2021.
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Posted by the Node Interviews, on 3 January 2021
This interview, the 87th in our series, was published in Development last year.
The patterning of stomata – the pores in the plant epidermis that facilitate gas exchange and water control – is regulated by a family of small secreted peptides. A new paper in Development analyses the effective ranges of two such peptides, borrowing a statistical technique used by astrophysicists to investigate the distribution and patterning of galaxies. We caught up with authors Emily Lo, who worked on the project when an undergraduate at the University of Washington (UW), and her supervisor Keiko Torii, who recently moved her lab from UW to The University of Texas at Austin (where she is Professor and Johnson & Johnson Centennial Chair in Plant Cell Biology), to hear more about the story.
Keiko, can you give us your scientific biography and the questions your lab is trying to answer?
KT: As a plant developmental biologist, I was always super fascinated by how dazzling arrays of functional, beautiful patterns emerge during development and how the external environment, where plants thrive, shapes the manifestation of such functional patterns. My main focus is to tackle such observations through understanding the molecular and genetic basis of cell-cell communication, ‘how plant cells talk to each other to generate functional patterns’.
I received my PhD and did my first short postdoc in Japan, where I identified the causal gene for the Arabidopsis mutant, erecta, which exhibits short stature and altered organ shape. It turned out that the ERECTA gene encodes a putative receptor kinase (collectively known as ‘Receptor-like Kinase’ or ‘RLK’), and it was the first report that this type of putative peptide receptor regulates plant growth and development. Later, after I obtained a tenure-track Assistant Professor position at the UW in Seattle, our research elucidated that ERECTA-family RLKs perceive a family of peptides to enforce proper stomatal patterning, which is the basis of this work.
In the Fall of 2019, I accepted the Johnson & Johnson Centennial Chair in Plant Cell Biology at the Department of Molecular Biosciences, The University of Texas at Austin. Currently I am also a Howard Hughes Medical Investigator.
And Emily – how did you come to work in Keiko’s lab on this project?
EL: I was lucky enough to be hired as an undergrad in Keiko’s lab during my freshman year at UW, and I stayed on until I graduated. It’s a rare opportunity to have such a long research experience as an undergrad, so I was able to devote a substantial amount of time to this project. Keiko introduced me to this fascinating project using mosaic fluorescent sectors to track peptide expression, which had been initiated by Dr. Takeshi Kuroha, a previous postdoctoral fellow, and Janelle Sagawa, a previous undergrad researcher (both acknowledged in the manuscript). So right away I could start growing seedlings, generating these mosaic sectors, and imaging on the confocal microscope. It was great fun! I graduated before we were able to complete the project, so Scott [Zeng] developed the majority of the SPACE pipeline after I left the lab.
How has your research been affected by the COVID-19 pandemic?
KT: Unfortunately, my lab and research program got hit really hard by the COVID-19 situation, because we had just relocated from Seattle WA to Austin TX right before the pandemic hit. Our brand-new lab at UT Austin was finally operating in the beginning of 2020 when we had to suddenly shut it down. Like myself, almost all the new lab members were new to Texas (or the Southern part of USA), and many were separated from family. So, staying at home in an unfamiliar city was stressful to everyone, and I truly thank my lab members for being positive and hanging together during this exceptionally difficult time. As for this manuscript, since we were at the phase of drafting a manuscript (lucky us!), Scott and I completed the manuscript during the full shut down phase, with thoughtful inputs from Emily and other co-authors. New online technology, such as Zoom, helped us work together, remotely.
EL: For this project, it was fortunate in that all experiments were completed and we were at the data analysis phase before COVID hit, so we were able to complete it through online communication (and because I’m located in Baltimore, I’d been communicating solely online anyway). For my current research at Hopkins, we were in an Essential-Only phase from March to June, in which no new experiments were allowed to begin; luckily, at that point I did have some computational analysis to catch up on. In mid-June we had our Phase-I reopening, so I’ve been able to resume many of my experiments, though of course progress is still limited by how much time we’re allotted in the lab.
Why have the signalling ranges of peptides like EPF1 and Stomagen been hard to assess, prior to your paper?
EL & KT: Whether secreted peptides or small chemical hormones, how far the signal moves is a fundamental question of pattern formation in development. But precisely quantifying the distance is not trivial. For direct observation, one could tag fluorescent proteins (or exogenously synthesize a peptide conjugated with a fluorophore). In a strict sense, however, such modifications change the size and property of peptides or chemical signals. Alternatively, one could develop sensors (such as a FRET sensor) that detect the existence of peptides or chemical signals.
We have previously shown that EPIDERMAL PATTERNING FACTOR (EPF) family members of secreted peptides fine-tune patterning of stomata on the plant epidermis by competitive binding to the same receptor. Because of the flat, two-dimensional nature of the developing leaf epidermis, we thought that our system would be a great model for understanding how far the secreted peptides influence tissue patterning, rather than directly observing its movement.
Can you give us the key results of the paper in a paragraph?
EL & KT: Using recombination-based mosaic sectors to overexpress signaling peptides EPF1 and Stomagen, which inhibit and promote stomatal development, respectively, we determined the effective ranges of these peptides in Arabidopsis cotyledons. We developed a quantitative pipeline to model stomatal distributions across the cotyledon in response to peptide overexpression, which we named SPACE (stomata patterning autocorrelation on epidermis), an homage to the astrophysics origin of the autocorrelation approach. We found that the inhibitor peptide EPF1 has a longer effective range than the activator peptide STOMAGEN, and that the patterning effects of peptide overexpression are limited to a local range rather than the global cotyledon.
How did you come upon the idea of borrowing an astrophysical technique to look at stomatal patterning?
KT: At the initial stage of our research, we were able to produce chimeras via heat-shock Cre/lox recombination, but we could not think of how to actually ‘calculate’ the effective distance of the peptides. Initially, we tried to set bin range (such as 100 μm, 200 μm, etc.) from each sector border. However, because of the complex geometry of pavement cells as well as the unique size, shape and location of individual sectors, we could not figure out how to normalize stomatal distribution surrounding each sector.
One morning in the kitchen, I was talking about this problem to my spouse, who is a theoretical physicist studying String Theory. When I was drawing a cartoon of a simple leaf (essentially an oval) with lots of stomata (essentially dots inside the oval), he told me, ‘this sounds familiar to me. I think my colleague, Miguel, is addressing the exact same problem – except that in his case, it’s the distribution of galaxies in the Universe’. I immediately e-mailed Prof. Miguel Morales of UW Physics. I thought that he might think I was crazy, but to my pleasant surprise, Miguel and his postdoc Dr Bryna Hazelton were very excited to hear about our research and the potential of the spatial autocorrelation statistics that they utilize for astrophysics in solving questions in plant development. Bryna mentored Emily in programming for the spatial autocorrelation analysis.
My Physics colleagues generously gave me the opportunity to give a 15 min talk to incoming Physics Graduate Students. I discussed the principles of spatial patterning in biological systems and introduced Alan Turing’s reaction-diffusion model; luckily, Scott remembered my brief talk and was curious enough to join my lab to tackle this problem after Emily’s graduation.
EL: For me it started when Keiko suggested we meet with Miguel and Bryna. When we explained that we were trying to generate a metric of epidermal spatial patterning, they almost immediately suggested looking into autocorrelation, an astrophysics method for analyzing galaxy distributions/patterning. Bryna works at the UW eScience Institute, and has a goal to empower the next generation of researchers and students to answer fundamental questions in complex or noisy data. Working with her to develop code to analyze our epidermal patterning questions was a really wonderful and fruitful experience, and that was the starting point for our collaboration and the development of the SPACE pipeline.
Why do you think the stomatal inhibitor EPF1 is able to travel farther than the activator Stomagen?
EL & KT: To clarify your question, the goal of our study was to determine how far these peptides act or have an effect, not necessarily the physical distance they travel. EPF1 has a longer range in terms of developmental outcome than Stomagen, but not necessarily diffusion distance. The question of their differing ranges is complex because stomatal lineage cells (which are induced by Stomagen) will themselves secrete EPF1, acting as a negative-feedback loop; in other words, the peptides are not acting in isolation. Our quantitative determination of peptide effective range is fascinating because in the Turing theory of pattern formation, a short-range activator often interacts with a longer-range inhibitor to achieve a self-regulating, periodic pattern. The relationship between Stomagen and EPF1 might be one such example of this effect to achieve regular, ordered stomatal spacing across the epidermis.
When doing the research, did you have any particular result or eureka moment that has stuck with you?
EL: After we’d established that the mosaic sector generation system indeed worked, we wanted to observe the potential global effects of peptide overexpression (from within the restricted mosaic sectors) across the entire cotyledon, so I switched to a confocal microscope that had tile-scanning functionality. The stitched image I got of the entire cotyledon surface was very beautiful; getting that first image was a hugely satisfying and validating moment for me.
Getting that first image was a hugely satisfying and validating moment for me
And what about the flipside: any moments of frustration or despair?
EL: The initial months were the most difficult experimentally for me. There were a lot of experimental skills that required finesse, for example sowing tiny Arabidopsis seeds individually on plates or mounting the cotyledons on glass slides completely flat without folding or tearing, etc. The way I overcame these challenges was practice and repetition: those are just skills that are gained slowly over time.
I understand you’ve now left Keiko’s lab – what are you doing now?
EL: I’m currently pursuing my PhD in Biomedical Engineering at Johns Hopkins, in the labs of Prof. Patrick Cahan and Prof. Andrew Feinberg. I study how changes in cell identity relate to cancer initiation in the context of pancreatic ductal adenocarcinoma: one of the most lethal malignancies in the US.
Even though I work on human disease research now, plant research is still very important to me, especially given the adaptations humans will have to make to agricultural practices in response to global climate change. Particularly, I think optimizing crop water consumption will be a key strategy in the next several decades to reach necessary agricultural yields in fluctuating environmental conditions.
Where will this story take the Torii lab?
KT: Stomatal patterning and distribution is critical for plant productivity and water use efficiency, and many different genetic and environmental factors (such as temperature, light, CO2 and drought) influence stomatal number, density and distribution. There is a long history in Plant Physiology of studying these traits. Yet, essentially, there are two ways to quantify these traits: stomata density (number of stomata per given area) and stomatal index (number of stomata per total epidermal cells). Different genetic backgrounds and environmental conditions may influence number, density or distribution in unique ways, but often such information is lost by simply presenting bar graphs of stomatal density and index. So, the natural next direction is to apply SPACE pipelines to describe different patterns of stomata, in different ages of Arabidopsis leaves or under different genetic/environmental conditions. Further harnessing the SPACE pipeline to quantitatively characterize stomatal patterning of agronomically important plant species, such as tomato and cereals, may reveal some important characteristics. Finally, we are looking for developmental biologists studying pattern formation of any systems who are brave enough to try out our SPACE pipeline to quantitatively characterize their systems.
Finally, let’s move outside the lab – what do you like to do in your spare time in Baltimore and Austin?
KT: Well…since I just relocated alone to a small one-bedroom apartment in Austin, and then the COVID-19 stay-at-home order was put in place, I really did not have much time to explore my new city. My spouse and children were supposed to move to Austin from Seattle this summer, but this got postponed due to COVID-19. I really hope that, when we (the USA) manage to get the pandemic under control, I can explore the Texas Hill Country and enjoy its natural beauty, and see bluebonnet wildflowers blooming for the first time in my life!
EL: I’m an avid baker, cook and gardener. During COVID-19, I’ve boarded the sourdough starter bandwagon as an at-home quarantine activity. And as much as possible, I’ve tried to stay in touch with friends and family across the country and the world by video chatting.
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